The Baseball America Prospect rankings were released last week, a list coveted by fans and media, but otherwise superfluous for the organizations themselves, who have their own rankings and plans for their players.

The Red Sox minor league system has some gems, but the conclusions that BA came to should be slightly disturbing. The list of the top ten prospects, as I say, seems strong, with names that we have heard regularly, such as Casey Kelly, the shortstop-turned-pitcher, and Jose Iglesias, the first round pick and shortstop of the future.

Ryan Westmoreland, an outfielder from Rhode Island, is listed as the best prospect in the system, the best hitter for average as well as the best athlete.

What should come as disturbing are what BA projects for the Sox offensive power hopes in the near future. Lars Anderson, last year’s top prospect, has long been touted as a power hitting first baseman, someone who can take the reigns at first while Kevin Youkilis moves to third. Unexpectedly, Anderson was listed as the Sox best power-hitting prospect.

Wait a minute. Lars Anderson?? The same Lars Anderson who dropped four spots from last year’s rankings? The same Lars Anderson who mustered a whopping nine home runs in 512 plate appearances last season at double-A Portland?

Can’t be. That can’t be the best in the Sox minor league system.

Believe it. The Sox are in serious offensive trouble. Their organizational depth is astronomically weighted against the power-hitting side of the game. As if this was not apparent through the raw rankings of the prospects, let’s take a look at what BA projects Boston’s 2012 lineup to look like.

The pitching situation is relatively constant with Casey Kelly the only new name in the rotation who is not there now. Victor Martinez, Dustin Pedroia and Youkilis remain the Sox’s catcher, second and third basemen respectively, and Jacoby Ellsbury stays in center field.

The parenthetical numbers represent the number of home runs that each player achieved last season, with all but Iglesias’ occurring in the Sox farm system. If we combine those numbers to the totals achieved last year by the holdovers (Martinez, Pedroia, Youkilis, and Ellsbury), we get an astounding 116 home runs.

116 home runs. That would have put the Sox squarely in 29th place last season, ahead of only the New York Mets, who had an absolutely horrible rash of injuries that affectively removed the top half of their lineup at some point during the season.

So while Kelly and Junichi Tazawa are the only two pitchers listed in BA’s top ten Sox prospects, their farm system is not currently in a position to provide them with a 30 home run hitter. It is very much weighted toward the Ellsbury-esque model of player – fast, athletic and a contact hitter.

What does this mean for the next few seasons? Well, firstly we must take everything that Theo Epstein says about acquiring a power hitter.

Yes, I am talking about Adrian Gonzalez. Gonzalez will command a top-flight package, one that would involve at least two of the names on that list of best prospects. But the fact is that the Red Sox are offensively solid for the next few years, with the exception of a big-time bat.

Even though Epstein has said many things about the Sox with respect to how they will deal with their farm system, the only player who is likely a true “untouchable” is Kelly. Kelly was listed as having the best fastball, curveball, changeup and overall control, despite only spending half of his first profession year as a pitcher. Past him, anyone is a possibility.

Given the affordable price tag ($4.75 million in ’10), his outstanding offensive prowess (106 home runs over the past three seasons) as well as his defense (back-to-back Gold Gloves in ’08-09), a package that would bring in Gonzalez would have to be of the caliber of Westmoreland, Lars Anderson and Alex Wilson (0.50 ERA in 13 starts for single-A Lowell Spinners in ’09). The package would also probably include a major league player or upper level minor leaguer who can contribute immediately, such as a Fernando Cabrera (Pawtucket closer last season) or a Manny Delcarmen.

For the Sox, there is no such thing as overpaying for a player such as Gonzalez.

The moves that the Boston Red Sox made at last Friday’s trading deadline gives them flexibility to choose from an array of line-ups each night. As they are preparing for a four-game showdown with the New York Yankees this weekend, the playoff run is very clearly upon them.

Victor Martinez is listed on the Red Sox roster as a catcher, although he played at only five more games behind the plate than at first for the Cleveland Indians before being traded. Pitchers often have difficulty adjusting to a new battery-mate after a trade, but a catcher has to learn an entire pitching staff’s strengths and weaknesses, a daunting task this late in the season.

That said, it is clear that the Sox’ best offensive line-up has Martinez at catcher, Kevin Youkilis at first base and Mike Lowell at third. In two of his three games with the Sox, however, Martinez has started at first, with Youkilis moving over to third, Jason Varitek doing the catching and Lowell playing left bench.

Varitek is the premier signal-caller in baseball. I say that without reserve, but not in reference to his hitting ability, or defensive signals, and certainly not his throwing arm. But rather that Varitek handles an entire pitching staff better than any other catcher in baseball, and calls a game with similar success.

Defensively, a catcher-first-third combination of Martinez-Youkilis-Lowell is roughly par with an assemblage of Varitek-Martinez-Youkilis. Varitek is no longer a Gold Glove catcher, and Lowell’s mobility and range is significantly reduced due to his off-season hip surgery.

Offensively, there is no debate that Martinez sports better numbers that Varitek. Martinez is an elite hitter at the position of catcher, and has hit in third in the Sox line-up.

The problem is that with Varitek tabbed as the team’s number one catcher, and any team wants their best starting line-up on the field in the playoffs, Varitek gets the starts during a playoff series. But that forces Youkilis over to third, which keeps Lowell out of the line-up.

Sox fans need no reminder that Lowell was the 2007 World Series MVP. But with his stint on the disabled list and constant talk of his off-season hip surgery, it may come as a bit of a surprise that Lowell is fourth on the team in batting average with an even .300. He has 11 home runs and 53 RBIs in 80 games this season.

That is a pretty solid bat to sit, especially for someone who has shown a lot of success in the playoffs (He racked up 15 RBI during the ’07 playoffs). Varitek, meanwhile, is headed toward another season batting average in the .220s.

Manager Terry Francona thus far has done a great job in managing the Sox’ line-up so that he rotates players in and out so that players with nagging injuries, like Varitek and Lowell, get the rest they need. In the playoffs, Lowell’s bat has to be in the line-up in place of Varitek at least half the time.

The implication that has for the Sox now is that Martinez needs to start catching the Sox front line starters, particularly Josh Beckett and Jon Lester. Beckett and Lester would undoubtedly go 1-2 in a playoff series. To avoid having Lowell’s bat on the bench for two games in a row, Martinez needs to be familiar enough to handle them in a playoff series.

Many teams that have productive hitting catchers, like the Indians (before the trade) and the Yankees, often use their regular catchers at another position. That sometimes leaves the team vulnerable because it becomes more difficult to pinch hit or run for that player.

If the Sox open a playoff series with Martinez as their everyday catcher, and Varitek on the bench, it gives them their best shot at winning the series. I do not underestimate Varitek’s value to the pitching staff, but for a very experienced staff like the Red Sox, Beckett and Lester can be relied on to handle their start.

What Beckett and Lester cannot do, and nor can Varitek apparently, is hit their weight. The Sox traded for a productive hitter because they were struggling offensively. Varitek and pitching coach John Farrell can micromanage their starters from the dugout and not loose much from their pitching staff.

Lastly, I do not mean to keep Varitek out of the line-up completely. When Varitek does start, it gives the Sox two excellent pinch hitters in Lowell and Casey Kotchman. But the Sox are disadvantaging their team to have Varitek catch consecutive games at the expense of a much better offensive player like Martinez or Lowell.

Martinez is the biggest offensive pickup of the 2009 trading deadline. Martinez had a injury plagued 2008 season that lead to mediocre numbers, but he has picked it up again in 2009 and reestablished himself as one of the best offensive catchers in the game.

A switch-hitter, he gives the Sox excellent versatility in the line-up and on the field. While not official, it is expected that he will play predominantly at catcher and designated hitter. He is a better left-handed hitter, and that will allow the Sox to rotate Mike Lowell and Jason Varitek in the line-up against lefties.

The Sox gave up RHP Justin Masterson, who had been splitting the year in the bullpen and rotation, and minor league pitchers Nick Hadagone and Bryan Price.

Masterson was a solid cog of the Red Sox team, but often found himself as the odd man out. The Indians will probably utilize him as a starter, which is where most scouts see him headed, but the Sox were never in the position to give him a chance to develop in that respect.

Hadagone was the biggest chip the Sox gave up. A left-hander in class-A Greenville, Hadagone underwent Timmy John surgery and recently returned from the disabled list and was very impressive. Price is a right-handed pitcher also in Greenville.

The other trade, while it possesses less excitement, was much more peculiar. The Sox obtained Kotchman, traded as the major component of the deal that brought Mark Teixeira to the Angels, for recently acquired Adam LaRoche.

It is odd not because LaRoche only spent a few days with the Sox, or that the Sox traded him because of the surplus of first basemen the Sox possess after getting Martinez. It is strange that the Sox would trade him, an everyday player, for another left-handed first basemen used to playing everyday.

Terry Francona is going to have to do an incredible job of juggling the line-up to make sure everyone gets enough at-bats to be happy. Kevin Youkilis has to play everyday, an one would expect that Martinez is also going to be in the line-up everyday.

This means that somehow Francona has to rotate them so that Varitek, Mike Lowell and David Ortiz get playing time. Lowell’s time figures to be cut the most, as Youkilis will likely play most of him games at third base for the rest of the season.

Given Martinez’s poorer numbers against lefties, and Lowell and Varitek’s success, they will be playing against left-handers. But while Varitek has been described as a walking ice-pack and Lowell is coming off of hip surgery, they can’t be thrilled at the prospect of their playing time being reduced. Kotchman has likely drawn the shortest straw. His playing time will be significantly reduced as virtually every other player in this rotation can play multiple positions, where Kotchman is relegated to first only.

Back up catcher George Kotteras will return to triple-A Pawtucket. He is the personal catcher for knuckle-baller Tim Wakefield, who is on the disabled list. He won’t be activated for a few weeks, at which time the Sox will have to decide who should catch him.

To replace Masterson, the Sox have several immediate choices to pick from. Southpaw Javier Lopez was optioned down at the beginning of the season because of terrible struggles, but he has turned his season down in the minors. The Pawtucket Red Sox’ closer Fernando Cabrera is mowing down hitters with an ERA under two while being perfect in save chances. Lefty Hunter Jones and righty Michael Bowden have already pitched out of the bullpen this season for the Sox, and they also have Japanese prospect Junichi Tazawa.

Until Wakefield comes back from the DL, one of those triple-A relievers figures to replace the gap in the bullpen.

Heading into tonight’s game against Baltimore, the Sox are a significantly upgraded team both offensively and defensively. The only problem will be getting a group of good players fair playing time, which any manager will tell you is a good problem to have.